Variant report

Variant	rs13328175
Chromosome Location	chr5:58573566-58573567
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:58571211-58573626	Hela-S3	cervix:	n/a	n/a
2	MYC	chr5:58573517-58573670	MCF10A-Er-Src	breast:	n/a	n/a
3	MAX	chr5:58573368-58574371	A549	lung:	n/a	n/a

Variant related genes	Relation type
PDE4D	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10036406	0.81[CEU][hapmap]
rs10038599	0.84[CEU][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10055446	0.80[CEU][hapmap]
rs10060200	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs10061786	0.84[CEU][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10070294	0.83[CEU][hapmap];0.95[EUR][1000 genomes]
rs10075364	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10079396	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs13328160	0.91[CEU][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13328226	0.91[CEU][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13354210	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs17444059	0.83[CEU][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17528473	0.91[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17528634	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17724250	0.90[CEU][hapmap]
rs17780213	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17780584	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs17780740	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs17780836	1.00[JPT][hapmap]
rs1824159	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs2044419	1.00[ASN][1000 genomes]
rs2112959	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2194210	0.88[CEU][hapmap]
rs28529077	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56183128	1.00[ASN][1000 genomes]
rs57516309	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61683381	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881054	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72765953	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72765961	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72765990	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72765993	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72767710	1.00[ASN][1000 genomes]
rs9292201	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9686434	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598252	chr5:58487764-58618889	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1023628	chr5:58557950-58757438	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv917274	chr5:58565291-58814374	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58571000-58573800	Enhancers	Fetal Heart	heart
2	chr5:58571800-58579400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:58572000-58573600	Enhancers	Fetal Brain Male	brain
4	chr5:58572000-58573800	Enhancers	Placenta Amnion	Placenta Amnion
5	chr5:58572000-58582800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:58572200-58573600	Enhancers	Fetal Lung	lung
7	chr5:58572200-58573800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr5:58572200-58573800	Enhancers	Brain Hippocampus Middle	brain
9	chr5:58572200-58573800	Enhancers	Brain Substantia Nigra	brain
10	chr5:58572200-58574400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr5:58572200-58583000	Weak transcription	Left Ventricle	heart
12	chr5:58572400-58573600	Enhancers	Fetal Intestine Small	intestine
13	chr5:58572400-58573600	Weak transcription	Right Atrium	heart
14	chr5:58572400-58575800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr5:58572600-58573800	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr5:58572800-58573600	Active TSS	Primary hematopoietic stem cells	blood
17	chr5:58572800-58573600	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr5:58572800-58573600	Enhancers	Rectal Smooth Muscle	rectum
19	chr5:58572800-58573600	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr5:58572800-58575200	Weak transcription	Fetal Intestine Large	intestine
21	chr5:58572800-58577800	Enhancers	Hela-S3	cervix
22	chr5:58573000-58573800	Enhancers	Brain Cingulate Gyrus	brain
23	chr5:58573000-58573800	Enhancers	HUVEC	blood vessel
24	chr5:58573000-58574000	Flanking Active TSS	A549	lung
25	chr5:58573000-58574800	Enhancers	Psoas Muscle	Psoas
26	chr5:58573200-58573600	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr5:58573200-58573800	Enhancers	Stomach Smooth Muscle	stomach
28	chr5:58573200-58574000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr5:58573200-58574000	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr5:58573200-58576000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr5:58573400-58583400	Weak transcription	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links